Congrats on the JP!! I just got mine as my first pin about a month ago. I'm learning quite a bit reading this post, and am really glad mine didn't seem to have these issues because I would be lost. lol I will add that all the lights (that have the colored condoms) that are on top of the gate, bunker posts, t-rex markers in bottom left, etc were not converted to LED because the seller said they were notorious for not fitting correctly, falling out, and being too bright. I do have LEDs in most of the playfield and blue in the back GI ones, and if you play it in the dark for very long you'll swear you are going to have a seizure from all the bright flashing. It is gorgeous though.
I'll also add that mine had Cliffy protectors on the bunkers, and I ended up taking them off because it made the bunkers harder to hit and the ball would get stuck coming back out of the far left bunker. I don't know if they were just installed wrong or what, and they certainly looked much better with the protectors on, but it plays better without in my opinion.
For cheap mods, check into the Papo dinos on Amazon. For less than $45, I got the t-rex, raptor, and pteradon to add to the playfield and they look great. The t-rex fits in the back right corner, the raptor over the raptor kick, and the pteradon where the pteradactyls are now. You have to remove the t-rex when you lift the playfield because he is so large he barely clears the glass, but he looks super cool.